fixing clitk gamma for profiles

[clitk.git] / segmentation / clitkExtractLymphStationsFilter.txx

diff --git a/segmentation/clitkExtractLymphStationsFilter.txx b/segmentation/clitkExtractLymphStationsFilter.txx
index 03fb77ec2d614a4314b555290d41727459328965..ec93c098b3421ea3d8a9105f5677c1212771ed45 100644 (file)
--- a/segmentation/clitkExtractLymphStationsFilter.txx
+++ b/segmentation/clitkExtractLymphStationsFilter.txx
@@ -62,7 +62,11 @@ ExtractLymphStationsFilter():
   ExtractStation_2RL_SetDefaultValues();
   ExtractStation_3A_SetDefaultValues();
   ExtractStation_1RL_SetDefaultValues();
+  ExtractStation_4RL_SetDefaultValues();
+  ExtractStation_5_SetDefaultValues();
+  ExtractStation_6_SetDefaultValues();
 
+  // TODO
   ExtractStation_7_SetDefaultValues();
   ExtractStation_8_SetDefaultValues();
 }
@@ -121,36 +125,26 @@ GenerateOutputInformation() {
     this->StopSubStep();  
   }
 
-  // Extract Station3P
+  // Extract Stations
+  ExtractStation_1RL();
+  ExtractStation_2RL();
   ExtractStation_3P();
-
-  // Extract Station3A
   ExtractStation_3A();
-
-  // Extract Station2RL
-  ExtractStation_2RL();
-
-  // Extract Station1RL
-  ExtractStation_1RL();
+  ExtractStation_4RL();
+  ExtractStation_5();
+  ExtractStation_6();
 
   // ---------- TODO -----------------------
 
   // Extract Station8
-  ExtractStation_8();
+  //  ExtractStation_8();
 
   // Extract Station7
-  this->StartNewStep("Station 7");
-  this->StartSubStep();
-  ExtractStation_7();
-  this->StopSubStep();
-
-  if (0) { // temporary suppress
-    // Extract Station4RL
-    this->StartNewStep("Station 4RL");
-    this->StartSubStep();
-    //ExtractStation_4RL();
-    this->StopSubStep();
-  }
+  //this->StartNewStep("Station 7");
+  //this->StartSubStep();
+  //ExtractStation_7();
+  //this->StopSubStep();
+  
 }
 //--------------------------------------------------------------------
 
@@ -309,23 +303,6 @@ void ComputeImageBoundariesCoordinates(typename ImageType::Pointer image,
 //--------------------------------------------------------------------
 
 
-//--------------------------------------------------------------------
-template <class TImageType>
-void 
-clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_4RL() {
-  DD("TODO");
-  exit(0);
-  /*
-    WARNING ONLY 4R FIRST !!! (not same inf limits)
-  */    
-  ExtractStation_4RL_SI_Limits();
-  ExtractStation_4RL_LR_Limits();
-  ExtractStation_4RL_AP_Limits();
-}
-//--------------------------------------------------------------------
-
-
 //--------------------------------------------------------------------
 template <class ImageType>
 void 
@@ -1011,8 +988,8 @@ FindAntPostVesselsOLD()
   binarizedContour = clitk::CropImageAlongOneAxis<MaskImageType>(binarizedContour, 2, inf, sup, 
                                                         false, GetBackgroundValue());
   // Update the AFDB
-  writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mhd");
-  this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mhd");  
+  writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mha");
+  this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mha");
   this->WriteAFDB();
   return binarizedContour;
 
@@ -1099,10 +1076,10 @@ FindAntPostVessels2()
   typedef std::map<std::string, MaskImagePointer>::iterator MapIter;
   MapOfStructures["BrachioCephalicArtery"] = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicArtery");
   MapOfStructures["BrachioCephalicVein"] = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
-  MapOfStructures["CommonCarotidArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArteryLeft");
-  MapOfStructures["CommonCarotidArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArteryRight");
-  MapOfStructures["SubclavianArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryLeft");
-  MapOfStructures["SubclavianArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryRight");
+  MapOfStructures["CommonCarotidArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("LeftCommonCarotidArtery");
+  MapOfStructures["CommonCarotidArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("RightCommonCarotidArtery");
+  MapOfStructures["SubclavianArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("LeftSubclavianArtery");
+  MapOfStructures["SubclavianArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("RightSubclavianArtery");
   MapOfStructures["Thyroid"] = this->GetAFDB()->template GetImage<MaskImageType>("Thyroid");
   MapOfStructures["Aorta"] = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
   MapOfStructures["Trachea"] = this->GetAFDB()->template GetImage<MaskImageType>("Trachea");
@@ -1370,8 +1347,8 @@ FindAntPostVessels2()
                                                         false, GetBackgroundValue());
 
   // Update the AFDB
-  writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mhd");
-  this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mhd");  
+  writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mha");
+  this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mha");
   this->WriteAFDB();
   return binarizedContour;